A sign is seen outside the National Security Agency campus in Fort Meade, Md. (Patrick Semansky / AP)

WASHINGTON — An online magazine reported Wednesday that the National Security Agency and the FBI covertly scanned the emails of five prominent Muslim-Americans under the government’s secret surveillance program aimed at foreign terrorists and other national security threats.

The report in The Intercept, a venture by journalist Glenn Greenwald, said the targets included an attorney, a Republican political operative, a university professor and two civil rights activists. The Intercept said all five denied any involvement in terrorism or espionage and had not been accused of any crimes. The magazine questioned whether the government obtained legal permission for its surveillance.

The Intercept account said that a three-month investigation using classified documents obtained from former NSA contract systems analyst Edward Snowden showed that “the system for authorizing NSA surveillance affords the government wide latitude in spying on US citizens.” The article also said that some government training materials included a slur against Muslims.

NSA and Justice Department officials denied Wednesday that American activists are targeted for criticizing the government. While not discussing the individual cases, officials said Americans are only targeted for email surveillance if there is probable cause.

“It is entirely false that US intelligence agencies conduct electronic surveillance of political, religious or activist figures solely because they disagree with public policies or criticize the government, or for exercising constitutional rights,” the NSA and Justice said in a joint statement.

But the White House on Wednesday ordered national security agencies to review their training and policy manuals in light of the article’s assertion that a 2005 government training document contained an anti-Muslim slur.

“Upon learning of this matter, the White House immediately requested that the Director of National Intelligence undertake an assessment of Intelligence Community policies, training standards or directives that promote diversity and tolerance,” said Caitlin Hayden, a White House national security spokeswoman.

Hayden said that “the use of racial or ethnic stereotypes, slurs, or other similar language” was unacceptable. The government ordered a similar review in 2011 after several training instructors told national security and military participants that mainstream Muslims supported violence.

The Intercept report is not the first account to suggest Americans’ emails have been swept up by the government. Documents leaked by Snowden, now a fugitive in Russia from a US law enforcement investigation, have shown that emails and other electronic files from thousands of Americans were scanned by the NSA’s massive worldwide intercepts aimed at foreign users suspected of terror connections and other threats.

Declassified legal documents released over the past year by the Obama administration also acknowledged that Americans’ web traffic is accidentally swept up, but separated out by “minimization” techniques. A recent Washington Post report based on Snowden files warned that such accidental sweeps pick up far more US web traffic than officials have acknowledged and that the material can be held indefinitely by the government in secret repositories.

The Intercept account suggests that in addition to such accidental sweeps, American citizens are sometimes intentionally targeted under the same foreign-targeted surveillance. The magazine identified the targeted Muslim-Americans as lawyer Asim Ghafoor, GOP operative Faisal Gill, Rutgers University professor Hooshang Amirahmadi, activist Agha Saeed and Nihad Awad, executive director of the Council of American-Islamic Relations, a Muslim civil rights group.

All five raised questions in the account about why their emails would have been targeted by surveillance.